Examples of DotAlignedAlignment

Examples of org.broad.igv.sam.DotAlignedAlignment

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    public DotAlignedAlignment readNextRecord(AsciiLineReader reader) {
        String nextLine;
        try {
            while ((nextLine = reader.readLine()) != null) {
                DotAlignedAlignment alignment = createAlignment(nextLine);
                if (alignment != null) {
                    return alignment;
                }
            }
        } catch (IOException e) {
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Examples of org.broad.igv.sam.DotAlignedAlignment

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                    isNegative = fields[STRAND_COLUMN].equals("-");
                }
                if (nTokens > NAME_COLUMN) {
                    name = fields[NAME_COLUMN];
                }
                return new DotAlignedAlignment(chr, start, end, isNegative, name);
            } else {

                boolean isNegative = fields[STRAND_COLUMN].equals("-");
                return new DotAlignedAlignment(chr, start, end, isNegative);
            }
        } catch (NumberFormatException e) {
            System.out.println("Skipping line: " + nextLine);
            return null;
        }
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Examples of org.broad.igv.sam.DotAlignedAlignment

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            String chr = inputStream.readUTF();
            int start = inputStream.readInt();
            int end = inputStream.readInt();
            boolean negativeStrand = inputStream.readBoolean();
            return new DotAlignedAlignment(chr, start, end, negativeStrand);
        } catch (EOFException ex) {
            return null;
        } catch (IOException ex) {
            log.error("Error decoding alignment", ex);
            return null;
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